ArticleGenome biology and evolution2013
Missing data and influential sites: choice of sites for phylogenetic analysis can be as important as taxon sampling and model choice.
Article in Genome biology and evolution, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
11 citing papers in PubMed.
- OrthoPhyl-streamlining large-scale, orthology-based phylogenomic studies of bacteria at broad evolutionary scales.G3 (Bethesda, Md.) · 2024Article
- Reference Genome Choice and Filtering Thresholds Jointly Influence Phylogenomic Analyses.Systematic biology · 2024Article
- A Practical Guide to Design and Assess a Phylogenomic Study.Genome biology and evolution · 2022Article
- DNA Barcodes Combined with Multilocus Data of Representative Taxa Can Generate Reliable Higher-Level Phylogenies.Systematic biology · 2022Article
- Uneven Missing Data Skew Phylogenomic Relationships within the Lories and Lorikeets.Genome biology and evolution · 2020Article
- A 250 plastome phylogeny of the grass family (Poaceae): topological support under different data partitions.PeerJ · 2018Article
- RADseq dataset with 90% missing data fully resolves recent radiation ofEcology and evolution · 2017Article
- Contentious relationships in phylogenomic studies can be driven by a handful of genes.Nature ecology & evolution · 2017Article
- Maximum Likelihood Phylogenetic Inference is Consistent on Multiple Sequence Alignments, with or without Gaps.Systematic biology · 2016Article
- Genetic diversification of penaeid shrimp infectious myonecrosis virus between Indonesia and Brazil.Virus research · 2014Article
- Automated reconstruction of whole-genome phylogenies from short-sequence reads.Molecular biology and evolution · 2014Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Phylogenetic studies based on molecular sequence alignments are expected to become more accurate as the number of sites in the alignments increases. With the advent of genomic-scale data, where alignments have very large numbers of sites, bootstrap values close to 100% and posterior probabilities close to 1 are the norm, suggesting that the number of sites is now seldom a limiting factor on phylogenetic accuracy. This provokes the question, should we be fussy about the sites we choose to include in a genomic-scale phylogenetic analysis? If some sites contain missing data, ambiguous character states, or gaps, then why not just throw them away before conducting the phylogenetic analysis? Indeed, this is exactly the approach taken in many phylogenetic studies. Here, we present an example where the decision on how to treat sites with missing data is of equal importance to decisions on taxon sampling and model choice, and we introduce a graphical method for illustrating this.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.